Hello all!

I am attempting to use flowCore with a few single colored controls in order to automate compensation for a project I am working on. My intent was to use the spillover() with my controls (read in as a flowSet) to do this, as shown here.

spill_mat <- spillover(ordered_frames.bead, unstained = "Unstained Beads", patt = "-A", fsc = 
                   "FSC-A", ssc = "SSC-A", stain_match = "ordered")

When looking at the matrix spillover() produces versus the matrix that FlowJo produces using the same controls, I notice that the numbers are drastically different (spillover() produces much larger numbers). This leads me to my question of whether the spillover() function produces a compensation matrix or a spillover matrix.

From my understanding, a compensation matrix is the inverse of a spillover matrix and, in my case, should be easy to calculate from the spillover matrix. But from the documentation, it seem to use the terms spillover matrix and compensation matrix interchangeably.

Does anyone have any knowledge on what this function produces?